This has really been causing me and the teams i am commanding some problems lately. I am so sorry Krenzo you are gonna hate me for this but i have absolutely no idea what sets this off. Basically, i can tick and untick 'anyone can build' as many times as i like but my team still tells me that the vf is restricted. it seems to strike randomly but also it strikes a lot. sorry i couldnt provide more info. I leave it in your capable hands.
Try exitting and entering the CV. Also, how many VFs do you have when this happens? Correct me if I'm wrong, but AFAIK this setting is per vehicle factory.
ive noticed that on small games (2v2/3v3) if i leave the com to buildsomething, it sometimes autolocks the vf until i get back in.